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Introduce modular version.

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This commit is contained in:
Jan Eitzinger 2020-08-18 14:27:28 +02:00
parent b2b910ef64
commit e7869286d7
16 changed files with 2208 additions and 863 deletions
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4
include_CLANG.mk
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@ -7,11 +7,11 @@ ANSI_CFLAGS += -std=c99
ANSI_CFLAGS += -pedantic
ANSI_CFLAGS += -Wextra
CFLAGS = -O2 -g #$(ANSI_CFLAGS)
CFLAGS = -O3 #-g $(ANSI_CFLAGS)
ASFLAGS = -masm=intel
CXXFLAGS = $(CFLAGS)
FCFLAGS =
LFLAGS =
DEFINES = -D_GNU_SOURCE
DEFINES = -D_GNU_SOURCE -DALIGNMENT=64
INCLUDES =
LIBS =

20
src/allocate.c
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@ -2,7 +2,7 @@
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2019 RRZE, University Erlangen-Nuremberg
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
@ -27,6 +27,7 @@
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <errno.h>
void* allocate (int alignment, size_t bytesize)
@ -56,3 +57,20 @@ void* allocate (int alignment, size_t bytesize)
return ptr;
}
void* reallocate (
void* ptr,
int alignment,
size_t newBytesize,
size_t oldBytesize)
{
void* newarray;
newarray = allocate(alignment, newBytesize);
if(ptr != NULL) {
memcpy(newarray, ptr, oldBytesize);
free(ptr);
}
return newarray;
}

186
src/atom.c Normal file
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@ -0,0 +1,186 @@
/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* =======================================================================================
*/
#include <math.h>
#include <parameter.h>
#include <allocate.h>
#include <atom.h>
#include <util.h>
#define DELTA 20000
void createAtom(Atom *atom, Parameter *param)
{
double xlo = 0.0; double xhi = param->xprd;
double ylo = 0.0; double yhi = param->yprd;
double zlo = 0.0; double zhi = param->zprd;
atom->Natoms = 4 * param->nx * param->ny * param->nz;
atom->Nlocal = 0;
double alat = pow((4.0 / param->rho), (1.0 / 3.0));
int ilo = (int) (xlo / (0.5 * alat) - 1);
int ihi = (int) (xhi / (0.5 * alat) + 1);
int jlo = (int) (ylo / (0.5 * alat) - 1);
int jhi = (int) (yhi / (0.5 * alat) + 1);
int klo = (int) (zlo / (0.5 * alat) - 1);
int khi = (int) (zhi / (0.5 * alat) + 1);
ilo = MAX(ilo, 0);
ihi = MIN(ihi, 2 * param->nx - 1);
jlo = MAX(jlo, 0);
jhi = MIN(jhi, 2 * param->ny - 1);
klo = MAX(klo, 0);
khi = MIN(khi, 2 * param->nz - 1);
double xtmp, ytmp, ztmp, vxtmp, vytmp, vztmp;
int i, j, k, m, n;
int sx = 0; int sy = 0; int sz = 0;
int ox = 0; int oy = 0; int oz = 0;
int subboxdim = 8;
while(oz * subboxdim <= khi) {
k = oz * subboxdim + sz;
j = oy * subboxdim + sy;
i = ox * subboxdim + sx;
if(((i + j + k) % 2 == 0) &&
(i >= ilo) && (i <= ihi) &&
(j >= jlo) && (j <= jhi) &&
(k >= klo) && (k <= khi)) {
xtmp = 0.5 * alat * i;
ytmp = 0.5 * alat * j;
ztmp = 0.5 * alat * k;
if( xtmp >= xlo && xtmp < xhi &&
ytmp >= ylo && ytmp < yhi &&
ztmp >= zlo && ztmp < zhi ) {
n = k * (2 * param->ny) * (2 * param->nx) +
j * (2 * param->nx) +
i + 1;
for(m = 0; m < 5; m++) {
myrandom(&n);
}
vxtmp = myrandom(&n);
for(m = 0; m < 5; m++){
myrandom(&n);
}
vytmp = myrandom(&n);
for(m = 0; m < 5; m++) {
myrandom(&n);
}
vztmp = myrandom(&n);
if(atom->Nlocal == atom->Nmax) {
growAtom(atom);
}
atom->x[atom->Nlocal] = xtmp;
atom->y[atom->Nlocal] = ytmp;
atom->z[atom->Nlocal] = ztmp;
atom->vx[atom->Nlocal] = vxtmp;
atom->vy[atom->Nlocal] = vytmp;
atom->vz[atom->Nlocal] = vztmp;
atom->Nlocal++;
}
}
sx++;
if(sx == subboxdim) { sx = 0; sy++; }
if(sy == subboxdim) { sy = 0; sz++; }
if(sz == subboxdim) { sz = 0; ox++; }
if(ox * subboxdim > ihi) { ox = 0; oy++; }
if(oy * subboxdim > jhi) { oy = 0; oz++; }
}
}
void growAtom(Atom *atom)
{
int nold = atom->Nmax;
atom->Nmax += DELTA;
atom->x = (double*) reallocate(atom->x, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->y = (double*) reallocate(atom->y, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->z = (double*) reallocate(atom->z, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->vx = (double*) reallocate(atom->vx, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->vy = (double*) reallocate(atom->vy, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->vz = (double*) reallocate(atom->vz, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->fx = (double*) reallocate(atom->fx, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->fy = (double*) reallocate(atom->fy, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->fz = (double*) reallocate(atom->fz, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
}
/* void sortAtom() */
/* { */
/* binatoms(neighbor); */
/* int* binpos = neighbor->bincount; */
/* int* bins = neighbor->bins; */
/* int mbins = neighbor->mbins; */
/* int atoms_per_bin = neighbor->atoms_per_bin; */
/* for(int i=1; i<mbins; i++) { */
/* binpos[i] += binpos[i-1]; */
/* } */
/* double* new_x = (double*) malloc(Nmax * sizeof(double)); */
/* double* new_y = (double*) malloc(Nmax * sizeof(double)); */
/* double* new_z = (double*) malloc(Nmax * sizeof(double)); */
/* double* new_vx = (double*) malloc(Nmax * sizeof(double)); */
/* double* new_vy = (double*) malloc(Nmax * sizeof(double)); */
/* double* new_vz = (double*) malloc(Nmax * sizeof(double)); */
/* double* old_x = x; double* old_y = y; double* old_z = z; */
/* double* old_vx = vx; double* old_vy = vy; double* old_vz = vz; */
/* for(int mybin = 0; mybin<mbins; mybin++) { */
/* int start = mybin>0?binpos[mybin-1]:0; */
/* int count = binpos[mybin] - start; */
/* for(int k=0; k<count; k++) { */
/* int new_i = start + k; */
/* int old_i = bins[mybin * atoms_per_bin + k]; */
/* new_x[new_i] = old_x[old_i]; */
/* new_y[new_i] = old_y[old_i]; */
/* new_z[new_i] = old_z[old_i]; */
/* new_vx[new_i] = old_vx[old_i]; */
/* new_vy[new_i] = old_vy[old_i]; */
/* new_vz[new_i] = old_vz[old_i]; */
/* } */
/* } */
/* free(x); free(y); free(z); */
/* free(vx); free(vy); free(vz); */
/* x = new_x; y = new_y; z = new_z; */
/* vx = new_vx; vy = new_vy; vz = new_vz; */
/* } */

4
src/includes/allocate.h
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@ -24,10 +24,10 @@
*
* =======================================================================================
*/
#include <stdlib.h>
#ifndef __ALLOCATE_H_
#define __ALLOCATE_H_
extern void* allocate (int alignment, size_t bytesize);
extern void* reallocate (void* ptr, int alignment, size_t newBytesize, size_t oldBytesize);
#endif

41
src/includes/atom.h Normal file
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@ -0,0 +1,41 @@
/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* =======================================================================================
*/
#include <parameter.h>
#ifndef __ATOM_H_
#define __ATOM_H_
typedef struct {
int Natoms, Nlocal, Nghost, Nmax;
double *x, *y, *z;
double *vx, *vy, *vz;
double *fx, *fy, *fz;
} Atom;
extern void createAtom(Atom*, Parameter*);
extern void growAtom(Atom*);
#endif

45
src/includes/neighbor.h Normal file
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@ -0,0 +1,45 @@
/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* =======================================================================================
*/
#include <atom.h>
#include <parameter.h>
#ifndef __NEIGHBOR_H_
#define __NEIGHBOR_H_
typedef struct {
/* double cutneigh; // neighbor cutoff */
int every;
int ncalls;
int* neighbors;
int maxneighs;
int* numneigh;
} Neighbor;
extern void initNeighbor(Neighbor*, Parameter*);
extern void setupNeighbor(Parameter*);
extern void binatoms(Atom*);
extern void buildNeighbor(Atom*, Neighbor*);
#endif

46
src/includes/parameter.h Normal file
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@ -0,0 +1,46 @@
/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* =======================================================================================
*/
#ifndef __PARAMETER_H_
#define __PARAMETER_H_
typedef struct {
double epsilon;
double sigma6;
double temp;
double rho;
double mass;
int ntimes;
int nstat;
int every;
double dt;
double dtforce;
double cutforce;
double cutneigh;
int nx, ny, nz;
double xprd, yprd, zprd;
} Parameter;
#endif

36
src/includes/pbc.h Normal file
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@ -0,0 +1,36 @@
/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* =======================================================================================
*/
#include <atom.h>
#include <parameter.h>
#ifndef __PBC_H_
#define __PBC_H_
extern void initPbc();
extern void updatePbc(Atom*, Parameter*);
extern void updateAtomsPbc(Atom*, Parameter*);
extern void setupPbc(Atom*, Parameter*);
#endif

35
src/includes/thermo.h Normal file
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@ -0,0 +1,35 @@
/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* =======================================================================================
*/
#include <parameter.h>
#include <atom.h>
#ifndef __THERMO_H_
#define __THERMO_H_
extern void setupThermo(Parameter*, int);
extern void computeThermo(int, Parameter*, Atom*);
extern void adjustThermo(Parameter*, Atom*);
#endif

41
src/includes/util.h Normal file
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@ -0,0 +1,41 @@
/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* =======================================================================================
*/
#ifndef __UTIL_H_
#define __UTIL_H_
#ifndef MIN
#define MIN(x,y) ((x)<(y)?(x):(y))
#endif
#ifndef MAX
#define MAX(x,y) ((x)>(y)?(x):(y))
#endif
#ifndef ABS
#define ABS(a) ((a) >= 0 ? (a) : -(a))
#endif
extern double myrandom(int*);
#endif

929
src/main.c
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345
src/neighbor.c Normal file
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@ -0,0 +1,345 @@
/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* =======================================================================================
*/
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <neighbor.h>
#include <parameter.h>
#include <atom.h>
#define SMALL 1.0e-6
#define FACTOR 0.999
static double xprd, yprd, zprd;
static double bininvx, bininvy, bininvz;
static int mbinxlo, mbinylo, mbinzlo;
static int nbinx, nbiny, nbinz;
static int mbinx, mbiny, mbinz; // n bins in x, y, z
static int *bincount;
static int *bins;
static int mbins; //total number of bins
static int atoms_per_bin; // max atoms per bin
static double cutneigh;
static double cutneighsq; // neighbor cutoff squared
static int nmax;
static int nstencil; // # of bins in stencil
static int* stencil; // stencil list of bin offsets
static double binsizex, binsizey, binsizez;
static int coord2bin(double, double , double);
static double bindist(int, int, int);
/* exported subroutines */
void initNeighbor(Neighbor *neighbor, Parameter *param)
{
double lattice = pow((4.0 / param->rho), (1.0 / 3.0));
double neighscale = 5.0 / 6.0;
xprd = param->nx * lattice;
yprd = param->ny * lattice;
zprd = param->nz * lattice;
cutneigh = param->cutneigh;
nbinx = neighscale * param->nx;
nbiny = neighscale * param->ny;
nbinz = neighscale * param->nz;
nmax = 0;
atoms_per_bin = 8;
stencil = NULL;
bins = NULL;
bincount = NULL;
neighbor->maxneighs = 100;
neighbor->numneigh = NULL;
neighbor->neighbors = NULL;
}
void setupNeighbor(Parameter *param)
{
double coord;
int mbinxhi, mbinyhi, mbinzhi;
int nextx, nexty, nextz;
double xlo = 0.0; double xhi = xprd;
double ylo = 0.0; double yhi = yprd;
double zlo = 0.0; double zhi = zprd;
cutneighsq = cutneigh * cutneigh;
binsizex = xprd / nbinx;
binsizey = yprd / nbiny;
binsizez = zprd / nbinz;
bininvx = 1.0 / binsizex;
bininvy = 1.0 / binsizey;
bininvz = 1.0 / binsizez;
coord = xlo - cutneigh - SMALL * xprd;
mbinxlo = (int) (coord * bininvx);
if (coord < 0.0) {
mbinxlo = mbinxlo - 1;
}
coord = xhi + cutneigh + SMALL * xprd;
mbinxhi = (int) (coord * bininvx);
coord = ylo - cutneigh - SMALL * yprd;
mbinylo = (int) (coord * bininvy);
if (coord < 0.0) {
mbinylo = mbinylo - 1;
}
coord = yhi + cutneigh + SMALL * yprd;
mbinyhi = (int) (coord * bininvy);
coord = zlo - cutneigh - SMALL * zprd;
mbinzlo = (int) (coord * bininvz);
if (coord < 0.0) {
mbinzlo = mbinzlo - 1;
}
coord = zhi + cutneigh + SMALL * zprd;
mbinzhi = (int) (coord * bininvz);
mbinxlo = mbinxlo - 1;
mbinxhi = mbinxhi + 1;
mbinx = mbinxhi - mbinxlo + 1;
mbinylo = mbinylo - 1;
mbinyhi = mbinyhi + 1;
mbiny = mbinyhi - mbinylo + 1;
mbinzlo = mbinzlo - 1;
mbinzhi = mbinzhi + 1;
mbinz = mbinzhi - mbinzlo + 1;
nextx = (int) (cutneigh * bininvx);
if(nextx * binsizex < FACTOR * cutneigh) nextx++;
nexty = (int) (cutneigh * bininvy);
if(nexty * binsizey < FACTOR * cutneigh) nexty++;
nextz = (int) (cutneigh * bininvz);
if(nextz * binsizez < FACTOR * cutneigh) nextz++;
if (stencil) {
free(stencil);
}
stencil = (int*) malloc(
(2 * nextz + 1) * (2 * nexty + 1) * (2 * nextx + 1) * sizeof(int));
nstencil = 0;
int kstart = -nextz;
for(int k = kstart; k <= nextz; k++) {
for(int j = -nexty; j <= nexty; j++) {
for(int i = -nextx; i <= nextx; i++) {
if(bindist(i, j, k) < cutneighsq) {
stencil[nstencil++] =
k * mbiny * mbinx + j * mbinx + i;
}
}
}
}
mbins = mbinx * mbiny * mbinz;
if (bincount) {
free(bincount);
}
bincount = (int*) malloc(mbins * sizeof(int));
if (bins) {
free(bins);
}
bins = (int*) malloc(mbins * atoms_per_bin * sizeof(int));
}
void buildNeighbor(Atom *atom, Neighbor *neighbor)
{
int nall = atom->Nlocal + atom->Nghost;
/* extend atom arrays if necessary */
if(nall > nmax) {
nmax = nall;
if(neighbor->numneigh) free(neighbor->numneigh);
if(neighbor->neighbors) free(neighbor->neighbors);
neighbor->numneigh = (int*) malloc(nmax * sizeof(int));
neighbor->neighbors = (int*) malloc(nmax * neighbor->maxneighs * sizeof(int*));
}
/* bin local & ghost atoms */
binatoms(atom);
int resize = 1;
double* x = atom->x;
double* y = atom->y;
double* z = atom->z;
/* loop over each atom, storing neighbors */
while(resize) {
int new_maxneighs = neighbor->maxneighs;
resize = 0;
for(int i = 0; i < atom->Nlocal; i++) {
int* neighptr = &(neighbor->neighbors[i * neighbor->maxneighs]);
int n = 0;
double xtmp = x[i];
double ytmp = y[i];
double ztmp = z[i];
int ibin = coord2bin(xtmp, ytmp, ztmp);
for(int k = 0; k < nstencil; k++) {
int jbin = ibin + stencil[k];
int* loc_bin = &bins[jbin * atoms_per_bin];
for(int m = 0; m < bincount[jbin]; m++) {
int j = loc_bin[m];
if ( j == i ){
continue;
}
double delx = xtmp - x[j];
double dely = ytmp - y[j];
double delz = ztmp - z[j];
double rsq = delx * delx + dely * dely + delz * delz;
if( rsq <= cutneighsq ) {
neighptr[n++] = j;
}
}
}
neighbor->numneigh[i] = n;
if(n >= neighbor->maxneighs) {
resize = 1;
if(n >= new_maxneighs) {
new_maxneighs = n;
}
}
}
if(resize) {
printf("RESIZE %d\n", neighbor->maxneighs);
neighbor->maxneighs = new_maxneighs * 1.2;
free(neighbor->neighbors);
neighbor->neighbors = (int*) malloc(atom->Nmax * neighbor->maxneighs * sizeof(int));
}
}
}
/* internal subroutines */
double bindist(int i, int j, int k)
{
double delx, dely, delz;
if(i > 0) {
delx = (i - 1) * binsizex;
} else if(i == 0) {
delx = 0.0;
} else {
delx = (i + 1) * binsizex;
}
if(j > 0) {
dely = (j - 1) * binsizey;
} else if(j == 0) {
dely = 0.0;
} else {
dely = (j + 1) * binsizey;
}
if(k > 0) {
delz = (k - 1) * binsizez;
} else if(k == 0) {
delz = 0.0;
} else {
delz = (k + 1) * binsizez;
}
return (delx * delx + dely * dely + delz * delz);
}
int coord2bin(double xin, double yin, double zin)
{
int ix, iy, iz;
if(xin >= xprd) {
ix = (int)((xin - xprd) * bininvx) + nbinx - mbinxlo;
} else if(xin >= 0.0) {
ix = (int)(xin * bininvx) - mbinxlo;
} else {
ix = (int)(xin * bininvx) - mbinxlo - 1;
}
if(yin >= yprd) {
iy = (int)((yin - yprd) * bininvy) + nbiny - mbinylo;
} else if(yin >= 0.0) {
iy = (int)(yin * bininvy) - mbinylo;
} else {
iy = (int)(yin * bininvy) - mbinylo - 1;
}
if(zin >= zprd) {
iz = (int)((zin - zprd) * bininvz) + nbinz - mbinzlo;
} else if(zin >= 0.0) {
iz = (int)(zin * bininvz) - mbinzlo;
} else {
iz = (int)(zin * bininvz) - mbinzlo - 1;
}
return (iz * mbiny * mbinx + iy * mbinx + ix + 1);
}
void binatoms(Atom *atom)
{
int nall = atom->Nlocal + atom->Nghost;
double* x = atom->x;
double* y = atom->y;
double* z = atom->z;
int resize = 1;
while(resize > 0) {
resize = 0;
for(int i = 0; i < mbins; i++) {
bincount[i] = 0;
}
for(int i = 0; i < nall; i++) {
int ibin = coord2bin(x[i], y[i], z[i]);
if(bincount[ibin] < atoms_per_bin) {
int ac = bincount[ibin]++;
bins[ibin * atoms_per_bin + ac] = i;
} else {
resize = 1;
}
}
if(resize) {
free(bins);
atoms_per_bin *= 2;
bins = (int*) malloc(mbins * atoms_per_bin * sizeof(int));
}
}
}

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/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* =======================================================================================
*/
#include <stdlib.h>
#include <stdio.h>
#include <pbc.h>
#include <atom.h>
#include <allocate.h>
#define DELTA 20000
static int NmaxGhost;
static int *BorderMap;
static int *PBCx, *PBCy, *PBCz;
static void growPbc();
void growPbc()
{
int nold = NmaxGhost;
NmaxGhost += DELTA;
BorderMap = (int*) reallocate(BorderMap, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
PBCx = (int*) reallocate(PBCx, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
PBCy = (int*) reallocate(PBCy, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
PBCz = (int*) reallocate(PBCz, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
}
void initPbc()
{
NmaxGhost = 0;
BorderMap = NULL;
PBCx = NULL; PBCy = NULL; PBCz = NULL;
}
void updatePbc(Atom *atom, Parameter *param)
{
int nlocal = atom->Nlocal;
double* x = atom->x;
double* y = atom->y;
double* z = atom->z;
double xprd = param->xprd;
double yprd = param->yprd;
double zprd = param->zprd;
for(int i = 0; i < atom->Nghost; i++) {
x[nlocal + i] = x[BorderMap[i]] + PBCx[i] * xprd;
y[nlocal + i] = y[BorderMap[i]] + PBCy[i] * yprd;
z[nlocal + i] = z[BorderMap[i]] + PBCz[i] * zprd;
}
}
void updateAtomsPbc(Atom *atom, Parameter *param)
{
double* x = atom->x;
double* y = atom->y;
double* z = atom->z;
double xprd = param->xprd;
double yprd = param->yprd;
double zprd = param->zprd;
for(int i = 0; i < atom->Nlocal; i++) {
if(x[i] < 0.0) {
x[i] += xprd;
} else if(x[i] >= xprd) {
x[i] -= xprd;
}
if(y[i] < 0.0) {
y[i] += yprd;
} else if(y[i] >= yprd) {
y[i] -= yprd;
}
if(z[i] < 0.0) {
z[i] += zprd;
} else if(z[i] >= zprd) {
z[i] -= zprd;
}
}
}
#define ADDGHOST(dx,dy,dz) Nghost++; BorderMap[Nghost] = i; PBCx[Nghost] = dx; PBCy[Nghost] = dy; PBCz[Nghost] = dz;
void setupPbc(Atom *atom, Parameter *param)
{
double* x = atom->x; double* y = atom->y; double* z = atom->z;
double xprd = param->xprd;
double yprd = param->yprd;
double zprd = param->zprd;
double Cutneigh = param->cutneigh;
int Nghost = -1;
for(int i = 0; i < atom->Nlocal; i++) {
if (atom->Nlocal + Nghost + 7 >= atom->Nmax) {
growAtom(atom);
x = atom->x; y = atom->y; z = atom->z;
}
if (Nghost + 7 >= NmaxGhost) {
growPbc();
}
/* Setup ghost atoms */
/* 6 planes */
if (x[i] < Cutneigh) { ADDGHOST(+1,0,0); }
if (x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,0,0); }
if (y[i] < Cutneigh) { ADDGHOST(0,+1,0); }
if (y[i] >= (yprd-Cutneigh)) { ADDGHOST(0,-1,0); }
if (z[i] < Cutneigh) { ADDGHOST(0,0,+1); }
if (z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,0,-1); }
/* 8 corners */
if (x[i] < Cutneigh && y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(+1,+1,+1); }
if (x[i] < Cutneigh && y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(+1,-1,+1); }
if (x[i] < Cutneigh && y[i] >= Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,+1,-1); }
if (x[i] < Cutneigh && y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,-1,-1); }
if (x[i] >= (xprd-Cutneigh) && y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(-1,+1,+1); }
if (x[i] >= (xprd-Cutneigh) && y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(-1,-1,+1); }
if (x[i] >= (xprd-Cutneigh) && y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,+1,-1); }
if (x[i] >= (xprd-Cutneigh) && y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,-1,-1); }
/* 12 edges */
if (x[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(+1,0,+1); }
if (x[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,0,-1); }
if (x[i] >= (xprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(-1,0,+1); }
if (x[i] >= (xprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,0,-1); }
if (y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(0,+1,+1); }
if (y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,+1,-1); }
if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(0,-1,+1); }
if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,-1,-1); }
if (y[i] < Cutneigh && x[i] < Cutneigh) { ADDGHOST(+1,+1,0); }
if (y[i] < Cutneigh && x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,+1,0); }
if (y[i] >= (yprd-Cutneigh) && x[i] < Cutneigh) { ADDGHOST(+1,-1,0); }
if (y[i] >= (yprd-Cutneigh) && x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,-1,0); }
}
// increase by one to make it the ghost atom count
atom->Nghost = Nghost + 1;
}

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/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* =======================================================================================
*/
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <thermo.h>
static int *steparr;
static double *tmparr;
static double *engarr;
static double *prsarr;
static double mvv2e;
static int dof_boltz;
static double t_scale;
static double p_scale;
static double e_scale;
static double t_act;
static double p_act;
static double e_act;
static int mstat;
void setupThermo(Parameter *param, int natoms)
{
int maxstat = param->ntimes / param->nstat + 2;
steparr = (int*) malloc(maxstat * sizeof(int));
tmparr = (double*) malloc(maxstat * sizeof(double));
engarr = (double*) malloc(maxstat * sizeof(double));
prsarr = (double*) malloc(maxstat * sizeof(double));
mvv2e = 1.0;
dof_boltz = (natoms * 3 - 3);
t_scale = mvv2e / dof_boltz;
p_scale = 1.0 / 3 / param->xprd / param->yprd / param->zprd;
e_scale = 0.5;
printf("step\ttemp\t\tpressure\n");
}
void computeThermo(int iflag, Parameter *param, Atom *atom)
{
double t = 0.0, p;
double* vx = atom->vx;
double* vy = atom->vy;
double* vz = atom->vz;
for(int i = 0; i < atom->Nlocal; i++) {
t += (vx[i] * vx[i] + vy[i] * vy[i] + vz[i] * vz[i]) * param->mass;
}
t = t * t_scale;
p = (t * dof_boltz) * p_scale;
int istep = iflag;
if(iflag == -1){
istep = param->ntimes;
}
if(iflag == 0){
mstat = 0;
}
steparr[mstat] = istep;
tmparr[mstat] = t;
prsarr[mstat] = p;
mstat++;
fprintf(stdout, "%i\t%e\t%e\n", istep, t, p);
}
void adjustThermo(Parameter *param, Atom *atom)
{
/* zero center-of-mass motion */
double vxtot = 0.0; double vytot = 0.0; double vztot = 0.0;
double* vx = atom->vx; double* vy = atom->vy; double* vz = atom->vz;
for(int i = 0; i < atom->Nlocal; i++) {
vxtot += vx[i];
vytot += vy[i];
vztot += vz[i];
}
vxtot = vxtot / atom->Natoms;
vytot = vytot / atom->Natoms;
vztot = vztot / atom->Natoms;
for(int i = 0; i < atom->Nlocal; i++) {
vx[i] -= vxtot;
vy[i] -= vytot;
vz[i] -= vztot;
}
t_act = 0;
double t = 0.0;
for(int i = 0; i < atom->Nlocal; i++) {
t += (vx[i] * vx[i] + vy[i] * vy[i] + vz[i] * vz[i]) * param->mass;
}
t *= t_scale;
double factor = sqrt(param->temp / t);
for(int i = 0; i < atom->Nlocal; i++) {
vx[i] *= factor;
vy[i] *= factor;
vz[i] *= factor;
}
}

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/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* =======================================================================================
*/
#include <util.h>
/* Park/Miller RNG w/out MASKING, so as to be like f90s version */
#define IA 16807
#define IM 2147483647
#define AM (1.0/IM)
#define IQ 127773
#define IR 2836
#define MASK 123459876
double myrandom(int* idum)
{
int k= (*idum) / IQ;
double ans;
*idum = IA * (*idum - k * IQ) - IR * k;
if(*idum < 0) *idum += IM;
ans = AM * (*idum);
return ans;
}

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